The Nedbank Running Club star, who had boldly declared he would win the race, backed up his words with action by crossing the finish line at Pilditch Stadium in 2:52:01.
The outspoken runner, nicknamed “Mr Marathon” and “head of the table,” pocketed R200 000 for his triumph.
His trademark dance celebration at the finish line capped off a dominant performance in near-perfect running conditions, on a route that started at Marlboro Gautrain Station and ended in Tshwane.
Khonkhobe outpaced Tebogo Pelusa, who clocked 2:53:25 for second place, and Siboniso Sikhakhane, who grabbed third in 2:53:31.
"I told everyone at the launch that I was going to win, and today I delivered,” Khonkhobe told SABC Sport after the race.
“I trusted myself and my preparation. Thanks to Nedbank and my sponsors—I’m super excited. Around the 9km mark, I decided to make my move, and from there I knew no one would catch me.”
The victory comes as redemption after Khonkhobe’s disappointment at this year’s Comrades Marathon, where he led for long stretches but failed to finish.
His coach, Pio Mpolokeng, said the plan for City 2 City was carefully mapped out.
“We prepared for this one, and I said before that while the Soweto Marathon was uncertain, we were confident about the 50km,” Mpolokeng explained.
“From here, we want to expose him to international competition at the World Half-Marathon in March next year.
"If Soweto Marathon goes ahead, he will defend his title.